BTN3A2

protein-coding

butyrophilin subfamily 3 member A2, the group of V-set domain containing|Butyrophilins

Gene summary

This gene encodes a member of the immunoglobulin superfamily, which resides in the juxta-telomeric region of the major histocompatability class 1 locus and is clustered with the other family members on chromosome 6. The encoded protein may be involved in the adaptive immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]

MANE transcript

NM_007047.5

Inheritance

—

ClinVar variants

U:52B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr6:26,365,159-26,378,320

External References & Databases

Ensembl (ENSG00000186470)

Transcript & Mutation Effects

hg38 • Region Span ~13.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BTN3A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007047.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			52 clinvar	2 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	2	1	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 158 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007047.5	RefSeq	NP_008978.2	7	MANE Select
ENST00000377708.7	Ensembl	ENSP00000366937.2	7	MANE Select
NM_001197246.2	RefSeq	NP_001184175.1	7	Standard
NM_001197247.3	RefSeq	NP_001184176.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Butyrophilin (BTN) family interactions
Immune System
Adaptive Immune System

Biological Process

T cell mediated immunity
regulation of immune response
T cell receptor signaling pathway
interferon-gamma secretion

Molecular Function

signaling receptor binding

Cellular Component

plasma membrane
external side of plasma membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356386
Coding exons: 7
Length: 13160
Individuals with no LoFs: 116526
Homozygous LoFs: 230
Heterozygous LoFs: 8992
Defined: 125748
p: 0.0374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.575	158	180	0.879	0.00000972	2135
Missense (PolyPhen)		48	53.932	0.89002		714
Synonymous	0.640	65	71.9	0.904	0.00000440	661
Loss of Function	0.259	16	17.2	0.933	9.72e-7	190

Population LoF Frequency

Population	CAF	p-value	Status
African	0.070	0.070	notable
Latino/Admixed American	0.029	0.029	notable
Ashkenazi Jewish	0.054	0.054	notable
East Asian	0.0037	0.0037	notable
Finnish	0.012	0.012	notable
European (Non-Finnish)	0.042	0.041	notable
South Asian	0.048	0.048	notable
Other	0.043	0.044	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in T-cell responses in the adaptive immune response. Inhibits the release of IFNG from activated T-cells. {ECO:0000269|PubMed:21918970, ECO:0000269|PubMed:22767497}.;

Recessive Scores

pRec: 0.0717

Intolerance Scores

LoFtool: 0.836
RVIS EVS: 0.8
RVIS percentile EVS: 87.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0425

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium